[English] 日本語
Yorodumi
- SASDCN4: Collagenase ColH s2as2bs3 at pCa 3 (Collagenase ColH segement s2a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: SASBDB / ID: SASDCN4
SampleCollagenase ColH s2as2bs3 at pCa 3
  • Collagenase ColH segement s2as2bs3 (protein), s2as2bs3, Hathewaya histolytica
Function / homology
Function and homology information


tripeptidase activity / microbial collagenase / collagen metabolic process / collagen binding / metalloendopeptidase activity / endopeptidase activity / calcium ion binding / proteolysis / zinc ion binding / extracellular region
Similarity search - Function
Collagenase ColG, catalytic helper subdomain / Collagenase G catalytic helper subdomain / Peptidase M9A/M9B, collagenase, bacterial / Peptidase M9, collagenase, N-terminal domain / Collagenase / Peptidase family M9 N-terminal / PKD domain / Peptidase, C-terminal, archaeal/bacterial / Bacterial pre-peptidase C-terminal domain / Polycystic kidney disease (PKD) domain profile. ...Collagenase ColG, catalytic helper subdomain / Collagenase G catalytic helper subdomain / Peptidase M9A/M9B, collagenase, bacterial / Peptidase M9, collagenase, N-terminal domain / Collagenase / Peptidase family M9 N-terminal / PKD domain / Peptidase, C-terminal, archaeal/bacterial / Bacterial pre-peptidase C-terminal domain / Polycystic kidney disease (PKD) domain profile. / PKD domain / PKD domain superfamily / PKD/Chitinase domain / Repeats in polycystic kidney disease 1 (PKD1) and other proteins / Neutral zinc metallopeptidases, zinc-binding region signature. / Concanavalin A-like lectin/glucanase domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesHathewaya histolytica (bacteria)
Contact author
  • Christopher Ruth (University of Arkansas, Fayetteville, AR, USA)

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Models

Model #1290
Type: dummy / Software: (2.6.1) / Radius of dummy atoms: 2.50 A / Symmetry: P1 / Chi-square value: 1.017 / P-value: 0.000150
Search similar-shape structures of this assembly by Omokage search (details)

-
Sample

SampleName: Collagenase ColH s2as2bs3 at pCa 3 / Specimen concentration: 2.00-5.50
BufferName: 10mM HEPES 100mM NaCl 0.2mM EGTA / pH: 7.5 / Comment: pCa 3
Entity #688Name: s2as2bs3 / Type: protein / Description: Collagenase ColH segement s2as2bs3 / Formula weight: 34.2 / Num. of mol.: 1 / Source: Hathewaya histolytica / References: UniProt: Q46085
Sequence: GSPGIPGPNE GDSKNSLPYG KINGTYKGTE KEKIKFSSEG SFDPDGKIVS YEWDFGDGNK SNEENPEHSY DKVGTYTVKL KVTDDKGESS VSTTTAEIKD LSENKLPVIY MHVPKSGALN QKVVFYGKGT YDPDGSIAGY QWDFGDGSDF SSEQNPSHVY TKKGEYTVTL ...Sequence:
GSPGIPGPNE GDSKNSLPYG KINGTYKGTE KEKIKFSSEG SFDPDGKIVS YEWDFGDGNK SNEENPEHSY DKVGTYTVKL KVTDDKGESS VSTTTAEIKD LSENKLPVIY MHVPKSGALN QKVVFYGKGT YDPDGSIAGY QWDFGDGSDF SSEQNPSHVY TKKGEYTVTL RVMDSSGQMS EKTMKIKITD PVYPIGTEKE PNNSKETASG PIVPGIPVSG TIENTSDQDY FYFDVITPGE VKIDINKLGY GGATWVVYDE NNNAVSYATD DGQNLSGKFK ADKPGRYYIH LYMFNGSYMP YRINIEGSVG R

-
Experimental information

BeamInstrument name: Advanced Light Source (ALS) 12.3.1 (SIBYLS)
City: Berkeley, CA / 国: USA / Type of source: X-ray synchrotron / Wavelength: 0.1127 Å / Dist. spec. to detc.: 1.5 mm
DetectorName: Pilatus3 X 2M / Pixsize x: 172 mm
Scan
Title: Collagenase ColH s2as2bs3 at pCa 3 / Measurement date: Oct 12, 2016 / Storage temperature: 4 °C / Cell temperature: 10 °C / Unit: 1/A /
MinMax
Q0.0125 0.5413
Distance distribution function P(R)
Sofotware P(R): GNOM 5.0 / Number of points: 333 /
MinMax
Q0.022577 0.207638
P(R) point1 333
R0 135.7
Result
Type of curve: extrapolated
ExperimentalPorodEstimatedEstimated method
MW34.2 kDa---
Volume-34.8 nm355 DAMFILT

P(R)P(R) errorGuinierGuinier error
Forward scattering, I016 0.08 15.56 0.11
Radius of gyration, Rg3.56 nm0.02 3.3 nm0.14

MinMax
D-13.6
Guinier point19 49

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more